Polygenic Score (PGS) ID: PGS001317

Predicted Trait
Reported Trait Vascular/heart problems diagnosed by doctor Heart attack
Mapped Trait(s) myocardial infarction (EFO_0000612)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1006150
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_BIN_FC1006150
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,030
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
195,990 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 6,356 cases
  • , 189,634 controls
]
 European UKB — — — white British ancestry —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM009078 PSS003775|
African Ancestry|
3,906 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack — AUROC: 0.72462 [0.66421, 0.78503] R²: 0.08703
Incremental AUROC (full-covars): -0.01046
PGS R2 (no covariates): 0.0002
PGS AUROC (no covariates): 0.50663 [0.44094, 0.57232]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009079 PSS003776|
East Asian Ancestry|
1,308 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack — AUROC: 0.78888 [0.66178, 0.91598] R²: 0.10419
Incremental AUROC (full-covars): -0.00694
PGS R2 (no covariates): 0.00068
PGS AUROC (no covariates): 0.53242 [0.37336, 0.69148]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009080 PSS003777|
European Ancestry|
18,556 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack — AUROC: 0.82479 [0.80685, 0.84274] R²: 0.1758
Incremental AUROC (full-covars): 0.00552
PGS R2 (no covariates): 0.00895
PGS AUROC (no covariates): 0.5766 [0.55039, 0.60282]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009081 PSS003778|
South Asian Ancestry|
5,342 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack — AUROC: 0.82696 [0.80387, 0.85004] R²: 0.22573
Incremental AUROC (full-covars): 0.00709
PGS R2 (no covariates): 0.00972
PGS AUROC (no covariates): 0.57536 [0.54237, 0.60835]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009082 PSS003779|
European Ancestry|
48,989 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vascular/heart problems diagnosed by doctor Heart attack — AUROC: 0.82191 [0.8123, 0.83152] R²: 0.18282
Incremental AUROC (full-covars): 0.01045
PGS R2 (no covariates): 0.01654
PGS AUROC (no covariates): 0.60058 [0.58663, 0.61453]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS003775 — —
[
  • 82 cases
  • , 3,824 controls
]
 — African unspecified — UKB —
PSS003776 — —
[
  • 11 cases
  • , 1,297 controls
]
 — East Asian — UKB —
PSS003777 — —
[
  • 465 cases
  • , 18,091 controls
]
 — European non-white British ancestry UKB —
PSS003778 — —
[
  • 299 cases
  • , 5,043 controls
]
 — South Asian — UKB —
PSS003779 — —
[
  • 1,611 cases
  • , 47,378 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)